Contacts of the strand formed by residues 228 - 231 (chain E) in PDB entry 2OHI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 228 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E ILE* 3.4 46.9 - - + +
9E SER* 4.7 2.9 - - - -
164E GLY 3.2 3.4 + - - +
165E ILE* 3.3 30.7 - - + +
166E LEU* 3.0 24.9 + - - +
182E LEU* 5.0 0.7 - - + -
226E ILE* 3.7 2.1 - - - +
227E GLN* 1.3 84.2 - - + +
229E ILE* 1.3 67.8 + - - +
230E ALA* 4.6 0.9 - - - +
236E ILE* 3.6 31.2 - - + -
237E TRP 3.2 9.2 - - - +
238E THR* 4.0 19.7 - - + -
240E PRO* 3.7 2.4 - - - +
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Residues in contact with ILE 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 3.4 21.1 - - + +
168E SER* 3.4 27.1 - - - +
172E PHE* 3.7 33.9 - - + -
223E LEU* 5.9 0.2 - - + -
226E ILE* 4.4 5.4 - - + -
228E MET* 1.3 76.1 - - - +
230E ALA* 1.3 59.2 + - - +
231E PRO* 3.4 5.1 - - + +
236E ILE* 3.6 1.9 - - - +
237E TRP* 2.8 46.9 + - + -
240E PRO* 3.6 23.4 - - + +
243E ILE* 4.3 7.0 - - + -
244E ILE* 3.8 28.0 - - + -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.8 3.6 - - + -
38E TYR* 3.4 34.8 - - + +
165E ILE* 4.5 7.0 - - + -
166E LEU 2.8 10.9 + - - +
167E PHE* 3.4 22.6 - - + +
168E SER* 3.2 18.7 + - - -
169E ASN 4.5 0.5 + - - -
228E MET* 4.1 0.6 - - + -
229E ILE* 1.3 73.1 - - - +
231E PRO* 1.4 65.6 - - - +
236E ILE* 4.3 11.4 - - + -
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Residues in contact with PRO 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ASN* 2.9 11.1 + - - +
38E TYR* 2.8 25.0 + - - +
168E SER* 3.5 4.0 - - - +
169E ASN* 3.3 15.7 - - - +
171E ALA 3.6 15.3 - - - +
172E PHE* 3.9 12.1 - - + +
173E GLY* 3.6 11.4 - - - +
229E ILE* 3.4 12.3 - - + +
230E ALA* 1.4 85.2 - - - +
232E SER* 1.3 57.6 + - - +
233E HIS 3.3 13.9 - - - +
235E GLN 3.3 26.7 - - - +
236E ILE* 4.1 1.3 - - - -
237E TRP* 4.2 3.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il